NAME

Bio::PhyloNetwork::FactoryX - Module to sequentially generate Phylogenetic Networks

SYNOPSIS

use strict;
use warnings;

use Bio::PhyloNetwork;
use Bio::PhyloNetwork::Factory;

# Will generate sequentially all the 4059 binary tree-child phylogenetic
# networks with 4 leaves

my $factory=Bio::PhyloNetwork::Factory->new(-numleaves=>4);

my @nets;

while (my $net=$factory->next_network()) {
  push @nets,$net;
  print "".(scalar @nets).": ".$net->eNewick()."\n";
}

DESCRIPTION

Sequentially builds a (binary tree-child) phylogenetic network each time next_network is called.

AUTHOR

Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es

SEE ALSO

Bio::PhyloNetwork

APPENDIX

The rest of the documentation details each of the object methods.

new

Title   : new
Usage   : my $factory = new Bio::PhyloNetwork::Factory();
Function: Creates a new Bio::PhyloNetwork::Factory
Returns : Bio::PhyloNetwork::RandomFactory
Args    : -numleaves => integer
           OR
          -leaves => reference to an array (of leaves names)
          -numhybrids => integer [default = numleaves -1]
          -recurse => boolean [optional]

Returns a Bio::PhyloNetwork::Factory object. Such an object will sequentially create binary tree-child phylogenetic networks each time next_network is called.

If the parameter -leaves=>\@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=>$numleaves, then the set of leaves will be "l1"..."l$numleaves".

If the parameter -numhybrids=>$numhybrids is given, then the generated networks will have at most $numhybrids hybrid nodes. Note that, necessarily, $numhybrids < $numleaves.

If the parameter -recurse=>1 is given, then all networks with number of hybrid nodes less or equal to $numhybrids will be given; otherwise only those with exactly $numhybrids hybrid nodes.

next_network

Title   : next_network
Usage   : my $net=$factory->next_network()
Function: returns a network
Returns : Bio::PhyloNetwork
Args    : none